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Magnesium in PDB 3f61: Crystal Structure of M. Tuberculosis Pknb LEU33ASP/VAL222ASP Double Mutant in Complex with Adp

Enzymatic activity of Crystal Structure of M. Tuberculosis Pknb LEU33ASP/VAL222ASP Double Mutant in Complex with Adp

All present enzymatic activity of Crystal Structure of M. Tuberculosis Pknb LEU33ASP/VAL222ASP Double Mutant in Complex with Adp:
2.7.11.1;

Protein crystallography data

The structure of Crystal Structure of M. Tuberculosis Pknb LEU33ASP/VAL222ASP Double Mutant in Complex with Adp, PDB code: 3f61 was solved by C.A.Mieczkowski, T.Alber, Tb Structural Genomics Consortium (Tbsgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.77 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 38.981, 51.542, 152.434, 90.00, 90.00, 90.00
R / Rfree (%) 20.3 / 22.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of M. Tuberculosis Pknb LEU33ASP/VAL222ASP Double Mutant in Complex with Adp (pdb code 3f61). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of M. Tuberculosis Pknb LEU33ASP/VAL222ASP Double Mutant in Complex with Adp, PDB code: 3f61:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3f61

Go back to Magnesium Binding Sites List in 3f61
Magnesium binding site 1 out of 4 in the Crystal Structure of M. Tuberculosis Pknb LEU33ASP/VAL222ASP Double Mutant in Complex with Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of M. Tuberculosis Pknb LEU33ASP/VAL222ASP Double Mutant in Complex with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg310

b:21.1
occ:1.00
 O2A A:ADP340 2.0 20.4 1.0
OD2 A:ASP156 2.0 22.5 1.0
O A:HOH411 2.1 19.9 1.0
OD1 A:ASN143 2.1 17.5 1.0
O1B A:ADP340 2.1 25.9 1.0
O A:HOH410 2.2 24.1 1.0
CG A:ASP156 3.2 22.1 1.0
PA A:ADP340 3.2 21.0 1.0
PB A:ADP340 3.2 27.4 1.0
CG A:ASN143 3.2 17.8 1.0
O3B A:ADP340 3.6 28.6 1.0
O3A A:ADP340 3.6 21.1 1.0
O5' A:ADP340 3.8 19.7 1.0
ND2 A:ASN143 3.8 17.7 1.0
CB A:ASP156 3.9 19.5 1.0
NZ A:LYS40 4.0 24.7 1.0
O A:HOH315 4.2 27.9 1.0
O A:HOH397 4.2 27.0 1.0
OD1 A:ASP156 4.2 29.0 1.0
O A:ALA142 4.3 18.6 1.0
CB A:ASN143 4.5 17.3 1.0
O1A A:ADP340 4.5 22.6 1.0
CG A:MET155 4.6 19.5 1.0
O2B A:ADP340 4.6 29.9 1.0
CA A:ASN143 4.6 17.1 1.0
C A:ALA142 4.8 17.7 1.0
CE A:LYS140 4.8 18.3 1.0
N A:ASN143 4.9 16.9 1.0
SD A:MET155 5.0 27.8 1.0

Magnesium binding site 2 out of 4 in 3f61

Go back to Magnesium Binding Sites List in 3f61
Magnesium binding site 2 out of 4 in the Crystal Structure of M. Tuberculosis Pknb LEU33ASP/VAL222ASP Double Mutant in Complex with Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of M. Tuberculosis Pknb LEU33ASP/VAL222ASP Double Mutant in Complex with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg311

b:25.8
occ:1.00
 O A:HOH385 2.9 30.6 1.0
O A:HOH404 3.0 31.9 1.0
N A:ALA142 3.1 18.4 1.0
CD A:PRO141 3.5 17.7 1.0
CB A:ALA142 3.5 17.6 1.0
CD A:ARG101 3.7 34.4 1.0
N A:PRO141 3.7 17.5 1.0
CG A:LYS140 3.8 16.2 1.0
CB A:LYS140 3.9 17.6 1.0
CA A:ALA142 3.9 17.1 1.0
CB A:PRO141 4.0 17.0 1.0
CD A:LYS140 4.0 18.3 1.0
C A:PRO141 4.0 17.8 1.0
CA A:PRO141 4.1 18.3 1.0
CG A:PRO141 4.2 19.1 1.0
CE2 A:TYR182 4.2 21.4 1.0
C A:LYS140 4.3 17.5 1.0
NE A:ARG101 4.3 39.3 1.0
CE A:LYS140 4.4 18.3 1.0
CB A:ARG101 4.4 24.1 1.0
CG A:ARG101 4.4 28.6 1.0
CZ A:TYR182 4.7 20.7 1.0
CA A:LYS140 4.7 17.1 1.0
OH A:TYR182 4.8 22.3 1.0
CD2 A:TYR182 4.8 21.0 1.0

Magnesium binding site 3 out of 4 in 3f61

Go back to Magnesium Binding Sites List in 3f61
Magnesium binding site 3 out of 4 in the Crystal Structure of M. Tuberculosis Pknb LEU33ASP/VAL222ASP Double Mutant in Complex with Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of M. Tuberculosis Pknb LEU33ASP/VAL222ASP Double Mutant in Complex with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg312

b:31.3
occ:1.00
 O A:HOH394 2.7 39.6 1.0
O1A A:ADP340 2.7 22.6 1.0
N A:SER23 3.0 19.4 1.0
N A:MET22 3.1 19.5 1.0
CA A:GLY20 3.1 17.9 1.0
C A:GLY20 3.2 17.7 1.0
N A:GLY21 3.2 18.9 1.0
O3A A:ADP340 3.4 21.1 1.0
O A:HOH412 3.4 31.2 1.0
N A:GLY20 3.5 17.8 1.0
CB A:SER23 3.6 19.4 1.0
PA A:ADP340 3.6 21.0 1.0
CA A:SER23 3.8 18.5 1.0
CA A:MET22 3.8 19.4 1.0
C A:MET22 3.8 19.2 1.0
OG A:SER23 3.8 21.6 1.0
O A:SER23 3.9 20.0 1.0
O A:GLY20 3.9 18.0 1.0
CB A:MET22 4.1 19.9 1.0
C A:GLY21 4.1 20.0 1.0
CA A:GLY21 4.2 19.1 1.0
O3B A:ADP340 4.2 28.6 1.0
O A:HOH358 4.3 26.2 1.0
C A:SER23 4.3 19.4 1.0
O A:HOH479 4.3 42.0 1.0
PB A:ADP340 4.5 27.4 1.0
C A:PHE19 4.7 17.5 1.0
O2A A:ADP340 4.7 20.4 1.0
O5' A:ADP340 4.8 19.7 1.0
C5' A:ADP340 4.8 19.1 1.0
O2B A:ADP340 5.0 29.9 1.0
O A:MET22 5.0 18.9 1.0

Magnesium binding site 4 out of 4 in 3f61

Go back to Magnesium Binding Sites List in 3f61
Magnesium binding site 4 out of 4 in the Crystal Structure of M. Tuberculosis Pknb LEU33ASP/VAL222ASP Double Mutant in Complex with Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of M. Tuberculosis Pknb LEU33ASP/VAL222ASP Double Mutant in Complex with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg313

b:53.5
occ:1.00
 CB A:ASN127 3.5 26.1 1.0
O A:HOH450 3.5 40.3 1.0
CA A:ALA267 3.6 21.8 1.0
CG A:ASN127 3.7 30.4 1.0
CD A:ARG270 3.8 26.1 1.0
CB A:ALA267 3.8 22.4 1.0
CA A:GLN124 4.0 22.5 1.0
O A:CYS123 4.0 19.8 1.0
OD1 A:ASN127 4.0 36.9 1.0
O A:HOH452 4.1 34.5 1.0
N A:ALA267 4.1 21.1 1.0
CG A:GLN124 4.1 27.6 1.0
N A:GLN124 4.3 21.4 1.0
C A:CYS123 4.3 20.4 1.0
CB A:ARG270 4.3 21.1 1.0
ND2 A:ASN127 4.3 29.2 1.0
CB A:GLN124 4.6 23.5 1.0
O A:ALA266 4.6 20.0 1.0
C A:ALA266 4.6 21.4 1.0
O A:HOH374 4.7 30.0 1.0
CG A:ARG270 4.7 23.0 1.0
C A:ALA267 4.7 21.9 1.0
CB A:CYS123 4.8 19.3 1.0
O A:ALA267 4.8 21.6 1.0
NE A:ARG270 4.9 28.7 1.0
CA A:ASN127 5.0 25.3 1.0

Reference:

C.Mieczkowski, A.T.Iavarone, T.Alber. Auto-Activation Mechanism of the Mycobacterium Tuberculosis Pknb Receptor Ser/Thr Kinase. Embo J. V. 27 3186 2008.
ISSN: ISSN 0261-4189
PubMed: 19008858
DOI: 10.1038/EMBOJ.2008.236
Page generated: Wed Aug 14 13:33:59 2024

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